mx-bluesky 1.5.9__py3-none-any.whl → 1.5.11__py3-none-any.whl

mx_bluesky/_version.py

@@ -28,7 +28,7 @@ version_tuple: VERSION_TUPLE
 commit_id: COMMIT_ID
 __commit_id__: COMMIT_ID
 
-__version__ = version = '1.5.9'
-__version_tuple__ = version_tuple = (1, 5, 9)
+__version__ = version = '1.5.11'
+__version_tuple__ = version_tuple = (1, 5, 11)
 
 __commit_id__ = commit_id = None

mx_bluesky/beamlines/aithre_lasershaping/goniometer_controls.py

@@ -53,9 +53,9 @@ def go_to_furthest_maximum(
 ) -> MsgGenerator:
     """Rotate to positive or negative maximum, whichever is further away"""
 
-    LIMIT_OF_TRAVEL = 3600
+    limit_of_travel = 3600
     current_value: float = yield from bps.rd(goniometer.omega.user_readback)
 
     yield from bps.mv(
-        goniometer.omega, -LIMIT_OF_TRAVEL if current_value > 0 else LIMIT_OF_TRAVEL
+        goniometer.omega, -limit_of_travel if current_value > 0 else limit_of_travel
     )

mx_bluesky/beamlines/i02_1/parameters/gridscan.py

@@ -20,7 +20,7 @@ class SpecifiedTwoDGridScan(
         return self.grid_1_spec
 
     @property
-    def FGS_params(self) -> ZebraGridScanParamsTwoD:
+    def fast_gridscan_params(self) -> ZebraGridScanParamsTwoD:
         return ZebraGridScanParamsTwoD(
             x_steps=self.x_steps,
             y_steps=self.y_steps,

mx_bluesky/beamlines/i04/experiment_plans/i04_grid_detect_then_xray_centre_plan.py

@@ -9,7 +9,7 @@ from dodal.common import inject
 from dodal.devices.aperturescatterguard import ApertureScatterguard, ApertureValue
 from dodal.devices.attenuator.attenuator import BinaryFilterAttenuator
 from dodal.devices.backlight import Backlight
-from dodal.devices.common_dcm import BaseDCM
+from dodal.devices.common_dcm import DoubleCrystalMonochromator
 from dodal.devices.detector.detector_motion import DetectorMotion
 from dodal.devices.eiger import EigerDetector
 from dodal.devices.fast_grid_scan import (
@@ -40,13 +40,13 @@ from mx_bluesky.common.device_setup_plans.setup_zebra_and_shutter import (
 )
 from mx_bluesky.common.experiment_plans.common_flyscan_xray_centre_plan import (
     BeamlineSpecificFGSFeatures,
-    construct_beamline_specific_FGS_features,
+    construct_beamline_specific_fast_gridscan_features,
 )
 from mx_bluesky.common.experiment_plans.common_grid_detect_then_xray_centre_plan import (
     grid_detect_then_xray_centre,
 )
 from mx_bluesky.common.experiment_plans.oav_snapshot_plan import (
-    setup_beamline_for_OAV,
+    setup_beamline_for_oav,
 )
 from mx_bluesky.common.external_interaction.callbacks.common.zocalo_callback import (
     ZocaloCallback,
@@ -97,7 +97,7 @@ def i04_grid_detect_then_xray_centre(
     attenuator: BinaryFilterAttenuator = inject("attenuator"),
     backlight: Backlight = inject("backlight"),
     beamstop: Beamstop = inject("beamstop"),
-    dcm: BaseDCM = inject("dcm"),
+    dcm: DoubleCrystalMonochromator = inject("dcm"),
     zebra_fast_grid_scan: ZebraFastGridScanThreeD = inject("zebra_fast_grid_scan"),
     flux: Flux = inject("flux"),
     oav: OAV = inject("oav"),
@@ -200,7 +200,7 @@ def get_ready_for_oav_and_close_shutter(
     yield from bps.wait(PlanGroupCheckpointConstants.GRID_READY_FOR_DC)
     group = "get_ready_for_oav_and_close_shutter"
     LOGGER.info("Non-udc tidy: Setting up beamline for OAV")
-    yield from setup_beamline_for_OAV(
+    yield from setup_beamline_for_oav(
         smargon, backlight, aperture_scatterguard, group=group
     )
     LOGGER.info("Non-udc tidy: Closing detector shutter")
@@ -243,14 +243,14 @@ def construct_i04_specific_features(
         xrc_composite.smargon.x,
         xrc_composite.smargon.y,
         xrc_composite.smargon.z,
-        xrc_composite.dcm.energy_in_kev,
+        xrc_composite.dcm.energy_in_keV,
     ]
 
     signals_to_read_during_collection = [
         xrc_composite.aperture_scatterguard,
         xrc_composite.attenuator.actual_transmission,
         xrc_composite.flux.flux_reading,
-        xrc_composite.dcm.energy_in_kev,
+        xrc_composite.dcm.energy_in_keV,
         xrc_composite.eiger.bit_depth,
     ]
 
@@ -264,10 +264,10 @@ def construct_i04_specific_features(
     set_flyscan_params_plan = partial(
         set_fast_grid_scan_params,
         xrc_composite.zebra_fast_grid_scan,
-        xrc_parameters.FGS_params,
+        xrc_parameters.fast_gridscan_params,
     )
     fgs_motors = xrc_composite.zebra_fast_grid_scan
-    return construct_beamline_specific_FGS_features(
+    return construct_beamline_specific_fast_gridscan_features(
         partial(
             setup_zebra_for_gridscan,
         ),

mx_bluesky/beamlines/i04/thawing_plan.py

@@ -62,7 +62,7 @@ def thaw_and_stream_to_redis(
                      defaults are always correct
     """
 
-    def switch_forwarder_to_ROI() -> MsgGenerator:
+    def switch_forwarder_to_roi() -> MsgGenerator:
         yield from bps.complete(oav_to_redis_forwarder, wait=True)
         yield from bps.mv(oav_to_redis_forwarder.selected_source, Source.ROI.value)
         yield from bps.kickoff(oav_to_redis_forwarder, wait=True)
@@ -75,7 +75,7 @@ def thaw_and_stream_to_redis(
         smargon,
         oav,
         oav_to_redis_forwarder,
-        switch_forwarder_to_ROI,
+        switch_forwarder_to_roi,
     )
 
 
@@ -110,14 +110,14 @@ def thaw_and_murko_centre(
                      defaults are always correct
     """
 
-    MURKO_RESULTS_GROUP = "get_results"
+    murko_results_group = "get_results"
 
-    def centre_then_switch_forwarder_to_ROI() -> MsgGenerator:
+    def centre_then_switch_forwarder_to_roi() -> MsgGenerator:
         yield from bps.complete(oav_to_redis_forwarder, wait=True)
 
         yield from bps.mv(oav_to_redis_forwarder.selected_source, Source.ROI.value)
 
-        yield from bps.wait(MURKO_RESULTS_GROUP)
+        yield from bps.wait(murko_results_group)
         x_predict = yield from bps.rd(murko_results.x_mm)
         y_predict = yield from bps.rd(murko_results.y_mm)
         z_predict = yield from bps.rd(murko_results.z_mm)
@@ -132,7 +132,7 @@ def thaw_and_murko_centre(
     yield from bps.mv(murko_results.sample_id, str(sample_id))
 
     yield from bps.stage(murko_results, wait=True)
-    yield from bps.trigger(murko_results, group=MURKO_RESULTS_GROUP)
+    yield from bps.trigger(murko_results, group=murko_results_group)
 
     yield from bpp.contingency_wrapper(
         _thaw_and_stream_to_redis(
@@ -143,7 +143,7 @@ def thaw_and_murko_centre(
             smargon,
             oav,
             oav_to_redis_forwarder,
-            centre_then_switch_forwarder_to_ROI,
+            centre_then_switch_forwarder_to_roi,
         ),
         final_plan=partial(bps.unstage, murko_results, wait=True),
     )
@@ -168,7 +168,7 @@ def _thaw(
         plan_between_rotations (MsgGenerator, optional): A plan to run between rotations
                                     of the smargon. Defaults to no plan.
     """
-    inital_velocity = yield from bps.rd(smargon.omega.velocity)
+    initial_velocity = yield from bps.rd(smargon.omega.velocity)
     new_velocity = abs(rotation / time_to_thaw) * 2.0
 
     def do_thaw():
@@ -180,7 +180,7 @@ def _thaw(
         yield from bps.rel_set(smargon.omega, -rotation, wait=True)
 
     def cleanup():
-        yield from bps.abs_set(smargon.omega.velocity, inital_velocity, wait=True)
+        yield from bps.abs_set(smargon.omega.velocity, initial_velocity, wait=True)
         yield from bps.abs_set(thawer.control, OnOff.OFF, wait=True)
 
     # Always cleanup even if there is a failure

mx_bluesky/beamlines/i24/jungfrau_commissioning/experiment_plans/do_darks.py

@@ -0,0 +1,123 @@
+import bluesky.preprocessors as bpp
+from bluesky import plan_stubs as bps
+from bluesky.utils import MsgGenerator
+from dodal.common import inject
+from dodal.devices.i24.commissioning_jungfrau import CommissioningJungfrau
+from ophyd_async.fastcs.jungfrau import (
+    AcquisitionType,
+    GainMode,
+    create_jungfrau_internal_triggering_info,
+    create_jungfrau_pedestal_triggering_info,
+)
+from pydantic import PositiveInt
+
+from mx_bluesky.beamlines.i24.jungfrau_commissioning.plan_stubs.plan_utils import (
+    fly_jungfrau,
+    override_file_path,
+)
+from mx_bluesky.common.utils.log import LOGGER
+
+PEDESTAL_DARKS_RUN = "PEDESTAL DARKS RUN"
+STANDARD_DARKS_RUN = "STANDARD DARKS RUN"
+
+
+def do_pedestal_darks(
+    exp_time_s: float = 0.001,
+    pedestal_frames: PositiveInt = 20,
+    pedestal_loops: PositiveInt = 200,
+    jungfrau: CommissioningJungfrau = inject("jungfrau"),
+    path_of_output_file: str | None = None,
+) -> MsgGenerator:
+    """Acquire darks in pedestal mode, using dynamic gain mode. This calibrates the offsets
+    for the jungfrau, and must be performed before acquiring real data in dynamic gain mode.
+
+    When Bluesky triggers the detector in pedestal mode, with pedestal frames F and pedestal loops L,
+    the acquisition is managed at the driver level to:
+    1. Acquire F-1 frames in dynamic gain mode
+    2. Acquire 1 frame in ForceSwitchG1 gain mode
+    3. Repeat steps 1-2 L times
+    4. Do the first three steps a second time, except use ForceSwitchG2 instead of ForceSwitchG1
+    during step 2.
+
+    A pedestal scan should be acquired when detector configuration and environmental conditions change, but due to small
+    in instabilities in beamline conditions, it is recommended to run a pedestal scan on roughly an hourly basis.
+
+    Args:
+        exp_time_s: Length of detector exposure for each frame.
+        pedestal_frames: Number of frames acquired per pedestal loop.
+        pedestal_loops: Number of times to acquire a set of pedestal_frames
+        jungfrau: Jungfrau device
+        path_of_output_file: Absolute path of the detector file output, including file name. If None, then use the PathProvider
+            set during Jungfrau device instantiation
+    """
+
+    @bpp.set_run_key_decorator(PEDESTAL_DARKS_RUN)
+    @bpp.run_decorator(md={"subplan_name": PEDESTAL_DARKS_RUN})
+    @bpp.stage_decorator([jungfrau])
+    def _do_decorated_plan():
+        if path_of_output_file:
+            override_file_path(jungfrau, path_of_output_file)
+
+        trigger_info = create_jungfrau_pedestal_triggering_info(
+            exp_time_s, pedestal_frames, pedestal_loops
+        )
+        LOGGER.info(
+            "Jungfrau will be triggered in pedestal mode and in dynamic gain mode"
+        )
+        yield from bps.mv(
+            jungfrau.drv.acquisition_type,
+            AcquisitionType.PEDESTAL,
+            jungfrau.drv.gain_mode,
+            GainMode.DYNAMIC,
+        )
+        yield from fly_jungfrau(
+            jungfrau,
+            trigger_info,
+            wait=True,
+            log_on_percentage_prefix="Jungfrau pedestal dynamic gain mode darks triggers received",
+        )
+
+    yield from _do_decorated_plan()
+
+
+def do_non_pedestal_darks(
+    gain_mode: GainMode,
+    exp_time_s: float = 0.001,
+    total_triggers: PositiveInt = 1000,
+    jungfrau: CommissioningJungfrau = inject("jungfrau"),
+    path_of_output_file: str | None = None,
+) -> MsgGenerator:
+    """Internally take a set of images at a given gain mode.
+
+    Non-pedestal darks are useful for detector panel cross-checks and for calculating masks.
+
+    Args:
+        gain_mode: Which gain mode to put the Jungfrau into before starting the acquisition.
+        exp_time_s: Length of detector exposure for each trigger.
+        total_triggers: Total triggers for the dark scan.
+        jungfrau: Jungfrau device
+        path_of_output_file: Absolute path of the detector file output, including file name. If None, then use the PathProvider
+            set during Jungfrau device instantiation
+    """
+
+    @bpp.set_run_key_decorator(STANDARD_DARKS_RUN)
+    @bpp.run_decorator(md={"subplan_name": STANDARD_DARKS_RUN})
+    @bpp.stage_decorator([jungfrau])
+    def _do_decorated_plan():
+        if path_of_output_file:
+            override_file_path(jungfrau, path_of_output_file)
+
+        trigger_info = create_jungfrau_internal_triggering_info(
+            total_triggers, exp_time_s
+        )
+
+        yield from bps.mv(jungfrau.drv.gain_mode, gain_mode)
+
+        yield from fly_jungfrau(
+            jungfrau,
+            trigger_info,
+            wait=True,
+            log_on_percentage_prefix=f"Jungfrau {gain_mode} gain mode darks triggers received",
+        )
+
+    yield from _do_decorated_plan()

mx_bluesky/beamlines/i24/jungfrau_commissioning/plan_stubs/__init__.py

@@ -0,0 +1 @@
+"""Jungfrau plan stubs should be used as part of Jungfrau experiment plans, and should not be run in isolation."""

mx_bluesky/beamlines/i24/jungfrau_commissioning/{do_external_acquisition.py → plan_stubs/do_external_acquisition.py}

@@ -9,7 +9,7 @@ from ophyd_async.fastcs.jungfrau import (
 )
 from pydantic import PositiveInt
 
-from mx_bluesky.beamlines.i24.jungfrau_commissioning.plan_utils import (
+from mx_bluesky.beamlines.i24.jungfrau_commissioning.plan_stubs.plan_utils import (
     fly_jungfrau,
     override_file_path,
 )
@@ -18,27 +18,28 @@ from mx_bluesky.beamlines.i24.jungfrau_commissioning.plan_utils import (
 def do_external_acquisition(
     exp_time_s: float,
     total_triggers: PositiveInt = 1,
-    output_file_name: str | None = None,
+    output_file_path: str | None = None,
     wait: bool = False,
     jungfrau: CommissioningJungfrau = inject("commissioning_jungfrau"),
 ) -> MsgGenerator[WatchableAsyncStatus]:
     """
     Kickoff external triggering on the Jungfrau, and optionally wait for completion.
 
-    Must be used within an open Bluesky run.
+    Any plan using this stub MUST stage the Jungfrau with the stage_decorator and open a run,
+    ideally using the run_decorator.
 
     Args:
         exp_time_s: Length of detector exposure for each frame.
-        total_triggers: Number of external triggers recieved before acquisition is marked as complete.
+        total_triggers: Number of external triggers received before acquisition is marked as complete.
         jungfrau: Jungfrau device
         output_file_name: Absolute path of the detector file output, including file name. If None, then use the PathProvider
             set during jungfrau device instantiation
         wait: Optionally block until data collection is complete.
     """
 
-    if output_file_name:
-        override_file_path(jungfrau, output_file_name)
+    if output_file_path:
+        override_file_path(jungfrau, output_file_path)
 
     trigger_info = create_jungfrau_external_triggering_info(total_triggers, exp_time_s)
-    status = yield from fly_jungfrau(jungfrau, trigger_info, wait)
+    status = yield from fly_jungfrau(jungfrau, trigger_info, wait=wait)
     return status

mx_bluesky/beamlines/i24/jungfrau_commissioning/{do_internal_acquisition.py → plan_stubs/do_internal_acquisition.py}

@@ -9,7 +9,7 @@ from ophyd_async.fastcs.jungfrau import (
 )
 from pydantic import PositiveInt
 
-from mx_bluesky.beamlines.i24.jungfrau_commissioning.plan_utils import (
+from mx_bluesky.beamlines.i24.jungfrau_commissioning.plan_stubs.plan_utils import (
     fly_jungfrau,
     override_file_path,
 )
@@ -26,7 +26,8 @@ def do_internal_acquisition(
     Kickoff internal triggering on the Jungfrau, and optionally wait for completion. Frames
     per trigger will trigger as rapidly as possible according to the Jungfrau deadtime.
 
-    Must be used within an open Bluesky run.
+    Any plan using this stub MUST stage the Jungfrau with the stage_decorator and open a run,
+    ideally using the run_decorator.
 
     Args:
         exp_time_s: Length of detector exposure for each frame.
@@ -42,5 +43,5 @@ def do_internal_acquisition(
         override_file_path(jungfrau, path_of_output_file)
 
     trigger_info = create_jungfrau_internal_triggering_info(total_frames, exp_time_s)
-    status = yield from fly_jungfrau(jungfrau, trigger_info, wait)
+    status = yield from fly_jungfrau(jungfrau, trigger_info, wait=wait)
     return status

mx_bluesky/beamlines/i24/jungfrau_commissioning/{plan_utils.py → plan_stubs/plan_utils.py}

@@ -2,7 +2,6 @@ from pathlib import PurePath
 from typing import cast
 
 import bluesky.plan_stubs as bps
-import bluesky.preprocessors as bpp
 from bluesky.utils import MsgGenerator
 from dodal.common.watcher_utils import log_on_percentage_complete
 from dodal.devices.i24.commissioning_jungfrau import CommissioningJungfrau
@@ -19,44 +18,38 @@ JF_COMPLETE_GROUP = "JF complete"
 
 
 def fly_jungfrau(
-    jungfrau: CommissioningJungfrau, trigger_info: TriggerInfo, wait: bool = False
+    jungfrau: CommissioningJungfrau,
+    trigger_info: TriggerInfo,
+    wait: bool = False,
+    log_on_percentage_prefix="Jungfrau data collection triggers received",
 ) -> MsgGenerator[WatchableAsyncStatus]:
     """Stage, prepare, and kickoff Jungfrau with a configured TriggerInfo. Optionally wait
     for completion.
 
-    Note that this plan doesn't include unstaging of the Jungfrau, and a run must be open
-    before this plan is called.
+    Any plan using this stub MUST stage the Jungfrau with the stage_decorator and open a run,
+    ideally using the run_decorator.
 
     Args:
     jungfrau: Jungfrau device.
-    trigger_info: TriggerInfo which should be acquired using jungfrau util functions create_jungfrau_internal_triggering_info
-        or create_jungfrau_external_triggering_info.
+    trigger_info: TriggerInfo which should be acquired using jungfrau util functions.
     wait: Optionally block until data collection is complete.
+    log_on_percentage_prefix: String that will be appended to the "percentage completion" logging message.
     """
 
-    @bpp.contingency_decorator(
-        except_plan=lambda _: (yield from bps.unstage(jungfrau, wait=True))
-    )
-    def _fly_with_unstage_contingency():
-        yield from bps.stage(jungfrau)
-        LOGGER.info("Setting up detector...")
-        yield from bps.prepare(jungfrau, trigger_info, wait=True)
-        LOGGER.info("Detector prepared. Starting acquisition")
-        yield from bps.kickoff(jungfrau, wait=True)
-        LOGGER.info("Waiting for acquisition to complete...")
-        status = yield from bps.complete(jungfrau, group=JF_COMPLETE_GROUP)
-
-        # StandardDetector.complete converts regular status to watchable status,
-        # but bluesky plan stubs can't see this currently
-        status = cast(WatchableAsyncStatus, status)
-        log_on_percentage_complete(
-            status, "Jungfrau data collection triggers recieved", 10
-        )
-        if wait:
-            yield from bps.wait(JF_COMPLETE_GROUP)
-        return status
+    LOGGER.info("Preparing detector...")
+    yield from bps.prepare(jungfrau, trigger_info, wait=True)
+    LOGGER.info("Detector prepared. Starting acquisition")
+    yield from bps.kickoff(jungfrau, wait=True)
+    LOGGER.info("Waiting for acquisition to complete...")
+    status = yield from bps.complete(jungfrau, group=JF_COMPLETE_GROUP)
 
-    return (yield from _fly_with_unstage_contingency())
+    # StandardDetector.complete converts regular status to watchable status,
+    # but bluesky plan stubs can't see this currently
+    status = cast(WatchableAsyncStatus, status)
+    log_on_percentage_complete(status, log_on_percentage_prefix, 10)
+    if wait:
+        yield from bps.wait(JF_COMPLETE_GROUP)
+    return status
 
 
 def override_file_path(jungfrau: CommissioningJungfrau, path_of_output_file: str):

mx_bluesky/beamlines/i24/serial/__init__.py

@@ -3,19 +3,20 @@ from mx_bluesky.beamlines.i24.serial.web_gui_plans.general_plans import (
     gui_move_backlight,
     gui_move_detector,
     gui_run_chip_collection,
+    gui_run_extruder_collection,
+    gui_set_fiducial_0,
     gui_set_zoom_level,
-    gui_sleep,
     gui_stage_move_on_click,
 )
 
-from .extruder.i24ssx_Extruder_Collect_py3v2 import (
+from .extruder.i24ssx_extruder_collect_py3v2 import (
     enter_hutch,
     initialise_extruder,
     laser_check,
     run_extruder_plan,
 )
-from .fixed_target.i24ssx_Chip_Collect_py3v1 import run_fixed_target_plan
-from .fixed_target.i24ssx_Chip_Manager_py3v1 import (
+from .fixed_target.i24ssx_chip_collect_py3v1 import run_fixed_target_plan
+from .fixed_target.i24ssx_chip_manager_py3v1 import (
     block_check,
     cs_maker,
     cs_reset,
@@ -56,9 +57,10 @@ __all__ = [
     # GUI plans
     "gui_stage_move_on_click",
     "gui_gonio_move_on_click",
-    "gui_sleep",
     "gui_move_detector",
     "gui_run_chip_collection",
     "gui_move_backlight",
     "gui_set_zoom_level",
+    "gui_set_fiducial_0",
+    "gui_run_extruder_collection",
 ]

mx_bluesky/beamlines/i24/serial/dcid.py

@@ -95,7 +95,7 @@ class DCID:
 
     Attributes:
         error:
-            If an error has occured. This will be set, even if emit_errors = True
+            If an error has occurred. This will be set, even if emit_errors = True
     """
 
     def __init__(
@@ -157,7 +157,7 @@ class DCID:
             xbeam, ybeam = beam_settings.beam_center_in_mm
 
             if isinstance(self.detector, Eiger):
-                startImageNumber = 1
+                start_image_number = 1
             else:
                 raise ValueError("Unknown detector:", self.detector)
 
@@ -201,7 +201,7 @@ class DCID:
                 "imageDirectory": image_dir,
                 "numberOfImages": num_images,
                 "resolution": resolution,
-                "startImageNumber": startImageNumber,
+                "startImageNumber": start_image_number,
                 "startTime": start_time.isoformat(),
                 "transmission": transmission,
                 "visit": self.parameters.visit.name,